Downpours left Ground Zero waterlogged yesterday, forcing cleanup efforts at the World Trade Center site to be temporarily halted.

The rains left huge puddles in the Ground Zero pit, which made it hard to continue the grim work of removing the last of the debris left behind by the fallen Twin Towers.

“Water began to collect near the middle of the pit where they have a recovery field where firefighters sift through debris,” said Sid Dinsay, a spokesman for the city Office of Emergency Management.

“In order to pump water, they had to stop operations for about two hours.”

Despite the delay, which wasn’t the first time rain stopped recovery work, the ceremony to mark the end of the eight-month cleanup will take place May 30.

The ceremony will start at 10:29 a.m., the moment the second of the Twin Towers collapsed.

Among the observances will be a bell rung for the firefighters lost in the line of duty, and an honor guard escorting an empty, flag-draped stretcher up the steel ramp out of the site, representing victims whose bodies weren’t found.